Functional variation in human Carbohydrate-Active enZYmes (hCAZymes) in relation to the efficacy of a FODMAP-reducing diet in IBS patients

Objective Limiting the dietary intake of carbohydrates poorly absorbed in the small intestine (FODMAPs) has therapeutic effects in some but not all irritable bowel syndrome (IBS) patients. We investigated genetic variation in human Carbohydrate-Active enZYmes (hCAZymes) genes in relation to the response to a FODMAP-lowering diet in the DOMINO study. Design hCAZy polymorphism was studied in IBS patients from the dietary (FODMAP-lowering; N=196) and medication (otilonium bromide; N=54) arms of the DOMINO trial via targeted sequencing of 6 genes of interest ( AMY2B , LCT , MGAM , MGAM2 , SI and TREH ). hCAZyme defective (hypomorphic) variants were identified via computational annotation using clinical pathogenicity classifiers. Age-and sex-adjusted logistic regression was used to test hCAZyme polymorphisms in cumulative analyses where IBS patients were stratified into carrier and non-carrier groups (collapsing all hCAZyme hypomorphic variants into a single bin). Quantitative analysis of hCAZyme variation was also performed, in which the number of hCAZyme genes affected by a hypomorphic variant was taken into account. Results In the dietary arm, the number of hypomorphic hCAZyme genes positively correlated with treatment response rate (P=0.03, OR=1.51 [CI=0.99-2.32]). In the IBS-D group (N=55), hCAZyme carriers were six times more likely to respond to the diet than non-carriers (P=0.002, OR=6.33 [CI=1.83-24.77]). These trends were not observed in the medication arm. Conclusions hCAZYme genetic variation may be relevant to the efficacy of a carbohydrate-lowering diet. This warrants additional testing and replication of findings, including mechanistic investigations of this phenomenon. WHAT IS KNOWN WHAT IS NEW HERE ### Competing Interest Statement Mauro D Amato received consulting fees and Mauro D Amato and Hassan Y Naim received unrestricted research grants from QOL Medical LLC. The sponsor had no role in the study design or in the collection, analysis, and interpretation of data. ### Clinical Trial NCT04270487 ### Funding Statement Supported by funding from: the Spanish Government MCIN/AEI/10.13039/501100011033 (PCI2021-122064-2A to MD A), the German Federal Ministry for Education and Research BMBF (01EA2208B to HYN and 01EA2208A to AF) and the Medical Research Council MRC (MR/W031213/1 to MC), under the umbrella of the European Joint Programming Initiative (A Healthy Diet for a Healthy Life) (JPI HDHL) and of the ERA-NET Cofund ERA-HDHL (GA No. 696295 of the EU Horizon 2020 Research and Innovation Programme); the Spanish Government MCIN/AEI/10.13039/501100011033 (PID2020-113625RB-I00 to MD A); the German Research Foundation DFG (NA331/13-1 to HYN and 390884018 for the Excellence Cluster (Precision Medicine in Chronic Inflammation) to AF); the DOMINO study was supported by the Belgian Health Care Knowledge Centre (ref number: 16001). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/IRB of Ethical Committee Research UZ/KU Leuven gave ethical approval for this work (protocol S59482), and all participants provided informed consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors. * AMY : (amylase) CADD : (Combined Annotation Dependent Depletion) DGBI : (Disorder of Gut-Brain Interaction) DOMINO : (Diet Or Medication in Irritable Bowel syndrome) FODMAPs : (Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols) GATK : (Genome Analysis Toolkit) GSA : (Global Screening Array) hCAZymes : (Human Carbohydrate-Active enZYmes) IBS : (Irritable Bowel Syndrome) IBS-SSS : (IBS-Symptom Severity Score) KEGG : (Kyoto Encyclopedia of Genes and Genomes) M-CAP : (Mendelian-Clinically Applicable Pathogenicity) MGAM : (Maltase-GlucoAMylase) NGS : (Next-Generation Sequencing) OB : (Otilonium Bromide) SI : (Sucrase-Isomaltase) SNP : (Single Nucleotide Polymorphism) SSRD : (Sucrose-and Starch-Reduced Diet) TREH : (Trehalase)